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FRED 2: an immunoinformatics framework for Python

Benjamin Schubert, Mathias Walzer, Hans-Philipp Brachvogel, András Szolek, Christopher Mohr, Oliver Kohlbacher
2016 Bioinformatics  
Here we present FRED 2, an open-source immunoinformatics framework offering easy and unified access to methods for epitope prediction and other immunoinformatics applications.  ...  FRED 2 is implemented in Python and designed to be extendable and flexible to allow rapid prototyping of complex applications. Availability and implementation: FRED 2 is available at http://fred-2  ...  We therefore developed FRamework for Epitope Detection (FRED 2) , an opensource, Python-based framework for computational immunology.  ... 
doi:10.1093/bioinformatics/btw113 pmid:27153717 pmcid:PMC4920123 fatcat:n6bpuacbijb33ee5rdnhi6drku

FRED--a framework for T-cell epitope detection

M. Feldhahn, P. Donnes, P. Thiel, O. Kohlbacher
2009 Bioinformatics  
We have developed FRED, an extendable, open source software framework for key tasks in immunoinformatics.  ...  FRED is implemented in Python in a modular way and allows the integration of external methods. Availability: FRED is freely available for download at  ...  CONCLUSIONS FRED is a valuable tool for performing large-scale analyses in immunoinformatics with different prediction methods and is also a software framework for the development of novel immunoinformatics  ... 
doi:10.1093/bioinformatics/btp409 pmid:19578173 pmcid:PMC2759545 fatcat:3a6mb3q7hfac7c27ucb7vmxgye

ImmunoNodes – graphical development of complex immunoinformatics workflows

Benjamin Schubert, Luis de la Garza, Christopher Mohr, Mathias Walzer, Oliver Kohlbacher
2017 BMC Bioinformatics  
FRED 2 is an immunoinformatics Python module that provides standardized interfaces to the immunoinformatics software.  ...  For further infromation, see the installation guide at ImmunoNodes. KNIME can be downloaded from  ... 
doi:10.1186/s12859-017-1667-z pmid:28482806 pmcid:PMC5422934 fatcat:4lbfdtf4xvg7jkpl6ox7vdvep4

Tracking the pipeline: immunoinformatics and the COVID-19 vaccine design

Shokouh Rezaei, Yahya Sefidbakht, Vuk Uskoković
2021 Briefings in Bioinformatics  
Here, we discuss how immunoinformatics can assist in the development of high-performance vaccines and drug discovery needed to curb the spread of SARS-CoV-2.  ...  With the onset of the COVID-19 pandemic, the amount of data on genomic and proteomic sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) stored in various databases has exponentially  ...  Mohammad Akhlaghi from Instituto de Astrofísica de Canarias (IAC) for help with the application of Maneage program.  ... 
doi:10.1093/bib/bbab241 pmid:34219142 fatcat:qkrlrtrnt5c6dndo3uv5lkyhae

The 18th European Symposium on Quantitative Structure–Activity Relationships

Anna Tsantili-Kakoulidou, Dimitris K Agrafiotis
2011 Expert Opinion on Drug Discovery  
Acknowledgements This research was partly funded by the EU FP7 project OpenTox -An Open Source Predictive Toxicology Framework (Health-F5-2008-200787) and the German Federal Ministry for the Environment  ...  Acknowledgements This research was partly funded by the EU FP7 project OpenTox -An Open Source Predictive Toxicology Framework (Health-F5-2008-200787) and the German Federal Ministry for the Environment  ...  R., Doytchinova, I Faculty of Pharmacy, Medical University of Sofia, 2 Dunav str, 1000 Sofia, Bulgaria T-cell epitope identification is a critical immunoinformatic problem for vaccine design.  ... 
doi:10.1517/17460441.2011.560604 pmid:22646021 fatcat:tb4bhvtnpzahxm4xba7iw4afuy